Mass Effect 2: Factor X
by Knight on Bald Mountain
Summary: UPDATE. This is NOT a new chapter. This is an update on the current state of the story. I apologize in advance for any confusion.
1. Prologue

Prologue

The _SSV Normandy_ was gone. Nothing more than a memory. Within just a couple minutes, the majestic work of engineering now became an empty husk of metal. It's broad and shining armor now burnt and torn. Anything that resembled a ship had now vanished. It would have been a spectacle to behold, had it not been for the deaths of the many crew members, and the loss of one particular soldier.

His name was Shepherd. Commander John Shepherd. A defender of the Alliance from a threat that it didn't even believe existed. His determination, skill and cunning brought an end to the horrific Reaper known only as _Sovereign_. Though the threat of the Reapers had been postponed, it was by no means over. As this expedient encounter with the _Normandy_ clearly proved. Of course, no one of the Council would admit it was them. In their willful ignorance, they'd wipe the memory of the Reapers away and replace it. Something less apocalyptic to keep the people from panicking.

Suffice to say, any hope of saving the known galaxy seemed lost. The one man who could stop it all, was dead and lost.

* * *

><p>Two years have passed since his death. What would happen next, no one in the Alliance could have anticipated.<p>

Cerberus happened. Held up as a radical human rights terrorist cell, they poured in billions of credits into the recovery and resurrection of the commander. Codenamed _The Lazarus Project_, the use of cybernetic implants, skin reconstruction and special fluids were all used to bring the dead man to life. It looked to be a lost cause. It seemed as if it all just wasn't enough. They had all the resources, but they needed something extra to make it all work.

Word was secretly leaked that a "top secret" organization needed donors to supply ample amounts of blood for the use of DNA splicing. Many volunteered. Some were accepted. Most were turned away. None of them worked. For a while, it seemed as though the project would stagnate and expire, but the Illusive Man, the person in charge of Cerberus, would rather spend another fortune than to see it all disappear.

That's when it happened. An unknown subject out of nowhere donated two pints of her blood. She charged an incredible amount of money for it, but it turned out to be exactly what was needed. She had the X factor. The scientists on the project had no idea what it was, and almost feared injecting it into the commander, but they had no other options. The moment they did it, the process began to work. Slowly and steadily, the corpse began to regenerate. Everything quickly began to fall into place.

Commander Shepherd's return was projected to be complete in a couple of weeks. The strange woman was contacted again; a request for another two pints of blood was made to finalize the project. She refused. Several attempts were made to sway her, but all were declined. It was not enough to stop the Illusive Man. He sent an operative to speak to her in person. He would get her into contact with him, and they would discuss it in private.

Though skeptical about the whole ordeal, she accepted. She was escorted to the Lazarus Research Station and lead to the conference room. There they left her alone and shut the door. That's when the hologram came up. There he was: the Illusive Man. Sitting comfortably in his chair while nonchalantly smoking his cigarette. For a good minute he didn't even say a word. He just observed the woman before her.

She wore a giant suit of armor, covering her entire body, adding almost a foot in height, he estimated. Had it not been for the green visor on her helmet, he might not have been able to even tell it was a woman. The way she stood lacked a basic femininity that he saw in Miranda Lawson, one of his chief officers. There was a presence that she exuded, just standing there waiting on him. He had many questions for her, and this was perhaps the only chance he'd have to ask them.

"I'm glad you accepted my offer to see me," he began, finishing another puff a smoke. "Let me first thank you for your incredibly generous donation to our project. It never would have been properly started without your aid."

"Thank you for you generous offer of credits." Her voice was soft but strong. The deeper tones suggested an elegance as well. "But now I'm afraid that I can't offer anymore."

"Certainly, you didn't come all the way here to just tell me that you weren't going to donate your blood."

"Perhaps I'm trusting that telling you directly will stop your attempts to take it by force."

"I instructed my people to convince you to give it to us _willingly_. If they attempted to kill you in the process, that was an error on _their_ part. Not mine."

"I've been studying your group for some time. You're very good at absolving yourself of any responsibility. I prefer working for people who are trustworthy."

"Then why did you come to us in the first place?"

The woman paused briefly before answering. "Because I needed the money."

"That can't be all," The Illusive Man grinned mildly, catching her in a half-truth. "Or else you didn't care about our trust then."

The woman remained silent, giving the Illusive Man another moment to try and read her. She had strong body control. Even under his mild interrogation, she made no apparent movements to indicate hesitation. Whatever it was she wanted, she did very well to hide it. Of course, the armor didn't help. "Would you mind removing you helmet? I would like to see who I'm negotiating with."

"Not a chance." A quick rejection with no follow up. The Illusive Man decided to move on.

"You know, you are a hard woman to track. I've had several of my operatives try to track your past. Would you like to hear what they found after three months of investigation?" The woman didn't respond verbally nor physically. "Nothing other than that you suddenly appeared in colonies near the Veil about a year ago."

There was a slight hint of movement inside the armor. Perhaps a chuckle. It was hard to tell. Still, he was not finished. "Now I pride myself in knowing everything about everyone I believe to be important, and when I can't do that, I am left to believe that there is something extraordinary about that person. It doesn't help that when you donated your blood the first time, even _my_ scientists don't know what to make of it."

"Perhaps I'm a by-product of a biological project." She chided him. The Illusive Man did not appreciate being talked down like child.

"Don't abuse your privilege to speak with me with your taunts. My scientists believe that your genetic code has been tampered with, for the better. We at Cerberus believe in anything that will serve the betterment of mankind, and that code could hold a vital key to make us the dominant species in the galaxy."

"Which is why you want two more pints of blood." The mysterious woman surmised.

"I've never hid my intentions. We _do _need two more pints of your blood to finish the regeneration of Commander Shepherd. I'm also asking that when you're ready to donate another two pints for genetic research, that you would do so. We are willing to double your payment for the second donation, and triple the third."

Again there was silence from the armored woman. She clearly had to think this one through. Perhaps the Illusive Man was starting to get through to her.

"I'm sorry, but I'm not going to donate my blood for your own research."

"Then will you at least do it for the commander? At least finish what you started."

"On one condition." She took a step closer towards the holographic projection of the seated gentleman. "I stay here on the station to make sure that it's used properly. If for even a second it's used outside the Lazarus Project, or if there is anymore attempts on my life, I'll make sure you never see the results."

"Agreed." He didn't even bother to consider anything else. The life of Commander Shepherd was of paramount importance, and everything else came second. "Send in Ms. Lawson and I'll have her make arrangements for your stay."

A mere second later, the door behind her opened, and the tall, well-figured woman strutted into the room, not even waiting for the other woman to leave. "You wanted to see me?"

"Miranda, please ensure that our donor has a place to stay on the station until Commander Shepherd is revived. She is our guest and will be treated as such."

"Of course, Illusive Man."

"Miranda." It was a command, not a question.

"Yes?"

"Do not listen in on my private conversations with guests."

"Of course, Illusive Man." She repeated herself, like a trained parrot. She turned to face the armored woman, raising an inviting arm out of the conference room. "This way, Ms. Aran."

The armored woman nodded as she began up the steps. "Just call me Samus."


	2. Chapter 1: Lazarus Crisis

AUTHOR'S NOTE: You might notice that events here are going to differ than those of the game. Check my profile for the whole story, but the point is that Samus' presence has changed everything, and events won't fall in place quite like they did before.

Chapter 1: Lazarus Crisis

At first, he felt nothing. Then came a mild rumbling, almost too subtle to feel. It started to get stronger, but it wasn't enough to wake him. That's when his ears began to pick it up. A voice was shouting at him, commanding him to wake up. He wasn't sure if it was all a dream or if it was reality. It took a moment for him to finally realize something wasn't right in the world.

He was alive.

He would have begun to ponder why that was, but somebody-a woman-was still shouting at him. "Commander Shepherd! You have to wake up!"

That's when he began to opened his eyes. Standing over him was someone in heavy battle armor. Through the green visor on the helmet, he saw the woman's eyes. They bore a look of deep concern. Ashley Williams gave him that look just before he went to grab Joker the day the Normandy was attacked. _How long ago was that? _He thought to himself. It had felt like a distant memory, but he remembered it so clearly.

"Commander Shepherd!" Her voice was now loud enough to leave a ringing in his ears. "The station is falling apart! I need you to get up! We don't have a lot of time before we all die!"

Shepherd wasn't one to take orders from unknown persons lightly, but as far as he could tell she was right. The rumblings he had heard from before were caused by explosions, and they were getting louder by the passing moment. If they were to escape, they'd need to move quickly.

Finally, Shepherd stood up. Now he could feel a throbbing pain in his head. He was almost certain it was going to explode.

"Quickly, there's some armor and a pistol set down just for you over here." The woman pointed with her arm towards the cache of armor. That's when he noticed that there was a giant cannon fixed on her right arm's armor. He didn't have much time to admire it, since he needed to suit up before anything happened. He took that moment to ask a quick question. "What's the situation?"

"Somebody has set charges at a number of critical areas on this station." The woman exclaimed, now in a more calm tone. "Then that somebody set off the LOKI and YMIR security mechs friend-foe identifier to keep everyone else occupied while he or she escapes."

"Is this a research station?" The commander asked, just as he was finishing suiting up. The woman nodded, which lead to his next question. "If someone wanted us all dead, why not just set off the self-destruct?"

"I don't know, but I assume it's because it wasn't Miranda who's trying to kill us. I believe she's the only one who could override such an order. Besides, I think this person wants you dead more than anything. You weren't supposed to be ready for another three days. My thoughts are he was hoping they'd come here first. You're lucky I saw them first, or they may have succeeded."

Shepherd nodded, but did not verbally reply. He still had some suspicions about his current situation. Perhaps the woman was just staging him for a death elsewhere. It didn't help that when he picked up his pistol, he noticed that it was empty. "This pistol doesn't have a thermal clip."

"I'm sure you'll find plenty on the dead LOKIs and YMIRs. Until then, I'll be taking care of them." She started heading for the door, but paused and turned back towards Shepherd. "The shuttle bay is a little ways off. Are you ready?"

"Just one question: What happened to me?"

"Long story short: you died. Two years later, we brought you back." The woman already began heading towards the door when she stopped. She turned to him once more to speak. "By the way, my name is Samus. Samus Aran."

Shepherd had originally intended to ask more questions while they ran, but he was still a bit disoriented, and lacked the focus to do so at the moment. The two quickly rushed through the next door, Samus checking all corners of the room before motioning it's safety. They made a turn up a ramp to follow a trail that Samus clearly knew very well. There was no question that she knew exactly where she was going. For a short while, they had virtually no complications. That's when the mechs began to appear. There were six of them, all gunning down at them with a monotone "HOSTILES DETECTED."

"Get down!" Samus shouted as she quickly engaged their adversaries. Shepherd did so, and watched in awe as the fearless woman simply ran towards them with her arm cannon firing rapid shots of what appeared to be electrical currents. Each one went down after about two shots each. The rounds that were fired after her deflected harmlessly off her armor. Within a matter of seconds, the mechs were smoldering on the ground.

Shepherd quickly got back up and grabbed the thermal clips left behind. He couldn't help but wonder what Samus' story could be, but while the explosions were still going off, he didn't wish to pry until they were safely away on a shuttle to anywhere but here.

Just a couple seconds later, they found another survivor. Taking cover behind a guardrail and firing his pistol at another set of mechs, was a dark-skinned human. The mechs hadn't yet spotted the two newcomers, so Shepherd took the opportunity to fire off his pistol at the mechs. Being dead definitely made him a bit rusty, but he still was quite capable at cutting them all down with speed and intensity. The younger man quickly spun his head around to see his rescuers.

"Shepherd? Aren't you still supposed to be under wraps?"

"That's what I'm told, but if this place is coming down, I don't think it really matters as long as we all get out of here alive."

"I suppose that's true. I also suppose that your friend here was the one to wake you."

"I did what I had to." Samus defended herself. "I doubt Miranda would have liked it if we all escaped save for him."

"Relax, Samus. I'm not accusing you. I'm just surprised you were able to do it. You look more like a battering ram than a biomedical specialist."

"I have my surprises, Jacob."

"I know we all have lot's of questions," Shepherd interjected, "but if this place is coming down like I've been told, we'd best get out now. We can talk along the way."

"You're right Shepherd." Jacob agreed. "You're going the right way to get to the shuttle bay. I guess I'll be tagging along then."

The trio expeditiously moved on. The first question came from Jacob. "Have either of you even seen Miranda yet?"

"Not a word." Samus replied. Shepherd, beginning to recover from his headache, responded with another question. "Is Miranda in charge of this station?"

"Technically." Jacob answered. "She was the one overseeing your regeneration. She along with Wilson, but he answered to her."

"And who do you all work for?"

Jacob had to pause first, debating whether or not he should respond truthfully. Samus didn't care, as she spoke quickly. "I'm a freelancer, but your friends here on the station are part of Cerberus."

Shepherd stopped completely. He had to think about this. "I remember Cerberus pretty well. They had some horrific experiments going on that I had to stop."

"I won't lie to you." Jacob interjected, knowing that deceiving him now would not bring him any good. "I myself don't trust everything that's been done, but they brought you back for a good reason. I myself only joined recently because the Alliance is not doing an adequate enough job protecting the galaxy."

"You're referring to the Reapers?" Jacob nodded. "All right, I'll follow for now, but I don't plan to help any of Cerberus' terrorist activities."

"That's all I'm asking right now."

"And don't forget that," Samus intervened. "Because I'm with Shepherd on this."

After a couple more rooms, Shepherd and the others ran into another group of mechs, hovering over a limping scientist. The three tried to catch him in time, but they were too short to reach.

"TARGET ACQUIRED."

"No! Stop!" The scientist pulled the trigger on his pistol to no effect. He was out of ammo. He almost silently murmured to himself as the mechs fired at him one last time. "Why do these things always backfire?"

"Dammit!" Jacob swore, causing the mechs to turn to face their new acquisition. The three humans quickly laid down a barrage of fire at the mechs, dropping them down before they even had a chance to fire back. Jacob headed over to see who they just lost. "It's Wilson. Didn't even stand a chance. If we'd been here just a little bit sooner."

"I don't know," Samus pondered. "He left a very brief blood trail, and it's leading from the mech control terminal."

"Maybe he was trying to shut them down." Jacob suggested.

"Maybe." Samus debilitated the possibility. "We should get going."

The others nodded and continued along the path towards the shuttles. Finally, they reached the cargo bay. The vast open area was littered with all sorts of boxes and crates. The shuttles would be up the walkway, but as luck would have it, one of the explosions had blocked the path to the shuttles. To make matters worse, they were being flanked by a score of mechs.

Samus turned around to face the ones behind them, firing another set of electric waves at her targets. Shepherd and Jacob took cover while slowly whittling away at the ones in front. The two soldiers worked well together, with Jacob using his biotic powers to pull the mechs helplessly forward, and Shepherd setting them off with a pair of rounds to the head of each one. The mechs were too stupid to use cover properly, having only limited programming, making it easier to eliminate their targets quickly. The only problem was that they were more persistent than most living threats, and they usually have a nonstop barrage of fire going over them. Though the two men took some minor hits, they were able to dispatch the last of their opponents with relative quickness and ease.

With the active threat out of the way, they now only needed to get rid of the debris in front of the shuttle bay door. Samus took the front on this problem. "Get behind me."

The two acknowledged as she began to charge her arm cannon. Once it reached a decent size, she fired off a missile. The blast annihilated the debris and even the door away, while still leaving the infrastructure intact. As the smoke cleared, they were surprised to see someone on the other side. It was Miranda Lawson.

"Well," she began, "I was wondering when you'd show up."

"If you were worried about time, you should have come after us, Miranda." Jacob accused. He was quite familiar with the way she ran things, and occasionally felt it necessary to remind her of such.

"In case you didn't notice, the door was blocked."

"So you just happened to be waiting in the shuttle bay before this attack had started?" Samus questioned.

"I knew the mechs were a distraction, and ran here to make sure that there _was_ and escape for us all."

"We don't have time for this." Shepherd declared. "We can argue on the shuttle."

"Shepherd's right . . . again." Jacob couldn't help but smile, knowing that the former corpse was already establishing his authority.

"Very well. Let's get going. Since you're up early, I'll need to ask you some questions along the way to see how you're holding up." She turned towards the armored woman. "I assume your work here is done?"

"Not likely. I'll be following you closely. Wherever Shepherd goes, _I_ go." She began to separate herself from the others, heading towards her own ship docked next to the shuttle. Shepherd couldn't help but noticed how particularly odd it looked. It's yellowish hue, and fighter-type size. Everything about that woman kept giving him more questions. She intrigued him.

* * *

><p>The shuttle ride was long and full of all sorts of questions. Miranda asking about Shepherd, recalling all his previous decisions from saving the council to leaving Lieutenant Alenko behind on Virmire. She picked his brain quite a lot. Then it was his turn, asking all about the Lazarus Project, what Cerberus wanted with him, but mostly about Samus. Miranda was quite happy to explain the details of the Lazarus Project, but explained that the Illusive Man, the head of the Cerberus, would explain what <em>he<em> wanted from him. As to who Samus really was, they simply weren't capable of answering. All that Miranda would say was that she was given an incredible large amount of credits to help donate to the project, but that she didn't trust Cerberus. It also became quite obvious to Shepherd that Miranda didn't like her at all.

They soon boarded a small gateway station in a nearby system. Miranda explained that she'd put Shepherd in contact with her boss, the Illusive Man, so that he knew what exactly was happening and what was expected of him. The last part did not sit well with the commander, but Samus told him that he was still his own boss, and to just ignore the latter part Miranda's statement.

Miranda made quick work setting up the conference hologram. Within a mere couple minutes, the three survivors of the Lazarus Project were seated in the waiting room while Shepherd marched into the Illusive Man's holochamber.

The room lit up as a grid-like analysis dictated where precisely to put the Illusive Man. Another couple seconds and it slowly generated the moving image of the Illusive Man. Still sitting on his favored chair and smoking another cigarette. Though it was the first time Shepherd, he could already tell that he rarely moved from that spot.

"Shepherd." His voice was almost casual, but still held an air of confidence. "It's good to see you alive."

"Illusive Man." Shepherd responded with equal confidence. His words simply floated in the air briefly, as if to see his reaction to hearing his name, or rather, what he was called. "I don't know why you brought me back, but I'm telling you now that I don't work with terrorists."

The Illusive Man took another puff of his cigarette. "Shepherd, you more than anyone know the threat that we face is larger than you and me. I ordered your recovery because not only are you a charismatic leader, but the only one who truly understands that threat."

"You're telling me your only thoughts were to protect the galaxy from the Reapers?" He could hardly believe him.

"Shepherd," The Illusive Man took his time explaining. "Your actions two years ago on the Citadel proved that humanity was ready to step up. You risked human lives to save the _Destiny Ascension_ and the Council, something I wouldn't have done, but you gained their trust.

"Now . . . " The Illusive Man paused as he took another puff. "They ignore the loss of _our_ colonies and pretend that the Reapers are still no more than a geth myth. Regardless of what you think of us here at Cerberus, we're the only ones that can help you."

Shepherd gave him an inquisitive look. "You said something about the 'loss of our colonies?'"

"Entire colonies are being abducted by unknown assailants. One hour they're running perfectly, in another we lose contact and then every member on that colony is gone without a trace. My sources believe that it's the work of the Reapers, but they're using someone else to do their dirt work.

"We have one lead right now." Out came another puff of smoke. "The colony Freedom's Progress. Our last communication with them was four hours ago. I'd suggest that you head there quickly before someone else investigates."

"_Is_ that a suggestion, or an order."

"As I've said before, I'm offering to _help_ you. I can only supply you with information and assistance. If you wish to reject it that's your prerogative, but you should head to Freedom's Progress first, and see it with your own eyes. I'll have Miranda and Jacob take you there on one of our shuttles."

"I'm not so sure I can trust them. They work for you, not for me."

"Miranda is loyal to me, yes, but she'll follow you as long as I tell her to. Jacob is more akin to you than you think. If you _can_ trust anyone here it's him."

"And what of the other woman, Samus?"

The Illusive Man sat silently for a second. He seemed to find that name a bit distasteful. "Her relation with us ended when you woke up. If you want her help, the choice is yours."

The Commander stood there in thought for a while. He wasn't sure how what to think of it all. The Illusive Man was quite accusatory of the Council and their attempts to cover up the Reapers. Though he was aware that they were still remise of the idea, he found it difficult to believe that they'd ignore such a threat of this magnitude. Perhaps the Illusive Man was right. At the very least, he could trust him to _help _him.

"Okay, I'll get over there as soon as possible, but keep in mind that I'm in charge of this operation."

"That's good, Shepherd. Miranda will have you flown over to Freedom's Progress whenever you're ready."

The hologram slowly began to fade. Shepherd took little time to leave the room. He even continued to walk past Miranda back to the shuttle while he informed her of their new task. "We're leaving for Freedom's Progress. I'm trusting your boss for now."

"If anything, we're taking a risk for trusting you." Miranda countered as she fell into step behind him. "I know you don't have Cerberus interests at heart."

"The galaxy is bigger than just us humans." Samus pointed out, starting ahead of them both. "I'll be following you again on my ship."

"Samus," Shepherd stopped her. "I don't know you, and though we both don't care for Cerberus, I'm not sure I want you along."

Samus sounded shocked at his response. "I saved your life, and not for any motive other than the fact that we _need_ you. Now I'm going to follow you whether you like it or not."

The armored woman stormed off towards her ship, giving Jacob ample time to catch up to the other two standing there. "I don't know about her, but I still got a feeling she's hiding something."

"And the Illusive Man isn't?" Shepherd asked rhetorically. He called out for Samus' attention. "Will you follow my orders?"

"To the letter."

"Then you can come along."

Under her helmet, a smile streaked across her face.


	3. Chapter 2: Halted Progress

Chapter 2: Halted Progress

Shepherd rested his head back against the chair. His headache was still causing some problems, and it didn't help that their landing on Freedom's Progress was taking longer than desired. Jacob seemed to have some difficulties compensating for the lack of space. All the docking bays were still occupied, and the closest clear landing was a good three kilometers away. Though not an unbearable distance at all, it was time that would be wasted. That left landing to open areas inside the colony itself. While Samus' ship seemed at ease to hover on top of a building, Jacob was attempting a slow descent in what appeared to be a merchant district covered with crates.

Eventually, they were able to land. Shepherd grabbed an assault rifle and sniper rifle off a weapons rack. He checked the scopes and barrels of both and when he was satisfied, he holstered them on his armor. He looked to both Jacob and Miranda who were ready as well. He motioned with his hand to move out. Shepherd took the point.

When they were outside, they could see Samus Aran on top of a building where she had landed. She hopped down with hardly a care and approached them. Shepherd followed suit and closed the gap. The armored woman spoke first. "All the buildings and structures seem to be in perfect condition. It's like there was no conflict at all."

"But everybody's still gone," Jacob pointed out. "So whoever is attacking colonies has been here and gone."

"Which means that they're able to clean them all without even a struggle." Miranda proposed. "If we're lucky, some must have hid and avoided detection."

"Searching for survivors sounds like the best idea." Shepherd determined. "We'll do that. I want us to stay together, but keep your eyes open for any movement."

With their new orders in, they all began to follow Shepherd around the colony. They took things slow, moving at a leisurely pace just to be sure they didn't overlook anything. After only a minute of trudging around empty buildings, they found something they did not expect.

Several LOKI mechs began to activate at their presence and began to attack. The four combatants quickly dispatched a couple of them, but were quickly flanked by a couple of FENRIS mechs. They charged directly at Samus. With one quick motion, they all leapt at her. Their taser devices shocked her armor, causing her to grunt, but it seemed to only slow her for a second while she turned to face her new targets. She fired her arm cannon at them as quickly and precisely as she could.

When she returned to the others, they had already finished the LOKIs. Jacob was the first to speak. "The security systems shouldn't be active. Someone has to be here."

Miranda pondered out loud. "We don't know for sure. They might have been activated during the assault."

"They would have fought back when they were attacked." Samus interjected.

"Since we don't know how the people were abducted, it's possible they never encountered anything." Miranda countered back.

"That probably would indicate that they were being abducted from space, which would also indicate that activating the mechs would have changed nothing." Samus fought back.

"I'm not trying to say how everything happened," Miranda took a step towards Samus. "I'm only rationalizing any possible outcome in a situation that we have little intel on."

"If you two are going to just argue the whole time, then I'll order you both back to the shuttle." Shepherd didn't even bother looking back at them as he continued walking and surveying the area. Samus and Miranda looked at him and then back at each other. Samus was the first to follow after him while Miranda took a moment before she did so.

Shepherd glanced back just to make sure she was now following. Of the three people accompanying him, he trusted her the least. He could tell by the way she spoke of the Illusive Man as they were on their way to the gateway station. The only thing he felt that she was honest about was her loyalty to that man. He did notice a couple other things, however. She had proven to be capable with a pistol in that last firefight, but she also showed off a number of biotic abilities that put most adepts to shame. And the way she looked, with her long, dark hair and powerful eyes. It was as if everything about her was trying to produce a presence of perfection.

Jacob, on the other hand, was different. He seemed to admire him, ready to listen and do whatever he said. He felt he could trust him. Plus, after listening to his story of when he was in the Alliance made Shepherd feel more at ease with him. Having Alliance training also showed his effectiveness in combat which seemed to overbear Miranda's. It helped make up for his weaker biotic abilities. His eyes didn't seem to show any presence at all. They were just always searching, as if they were looking for something and he still couldn't find it.

Then there was Samus. The mysterious woman had just taken a spot next to Shepherd. He still couldn't get a bead on what her intentions were. Since they were heading towards the cargo docks, he figured it'd be best to try and get to know her better. He started with something simple. "I've seen a full grown man go into shock when attacked by a group of FENRIS mechs that large . . . even in armor. How well does that thing protect you?"

Samus pondered briefly whether or not to answer, but she seemed to not mind this time. "It's the best there is. Of course, they're not made anymore, and are really hard to get your hands on. It took me four months just to hunt down this one in particular since my last one got abused."

"If it lasts as well as I've seen, how did it get 'abused' as you say?" Shepherd asked earnestly.

"I got infected. Some ridiculous parasitic virus got to me through the suit. The people trying to fix me up had to break it apart in certain places to get to me. It was still pretty effective, but not up to par with what I knew I'd be getting myself into."

"Well it certainly is a tough chunk of armor. Did all those armaments come with it?"

"With this one, yes. The last one I'd have to find upgrades here and there." She took a moment to point out a number of her weapons. "My arm cannon uses several different beam weapons along with a couple of missile components. You've seen me using my wave beam, which fires electrical bolts and occasionally will fire through walls when I charge it, but I also have an ice beam and plasma beam. Normally, though, I just use the power beam."

Samus was about to go on, but she stopped suddenly. She pointed towards one of the buildings. "My thermal scanner is picking up a number of humanoids in that structure."

"Perhaps they are survivors." Shepherd thought. "We'll start over there, but stay on your guard."

Shepherd motioned his fire team over in that direction. They quietly approached the building, setting themselves up for a breaching sequence, with Miranda and Jacob at the sides of the door, Samus as the point gunner, and Shepherd opening the door. On his count of three, he had the door opened and all his operatives aim inside. To everyone's surprise, they were greeted by more weapons. Weapons from quarians.

"Cerberus operatives!" One of them, a male, shouted. "Give us one reason not to shoot you now!"

"Dammit, Prazza!" Another one, female, swore as she walked at the lead and raised the mans gun from his current target. "This is _my_ mission, you listen to me."

She turned to face the intruders, and what she saw astonished her. "Shepherd? Is that really you?"

Shepherd quickly realized that the female quarian was none other than Tali'zorah vas Neema, a young engineer who had joined him on his hunt for Saren. She was even wearing the same protective environmental suit that she had the first day they had met. He remembered it very clearly, the young girl trying to deal with the Shadow Broker only to be ambushed by one of Saren's men. She dealt with him rather quickly, putting her combat training to the test. The young girl knew how to take care of herself, but still chose to follow Shepherd to the furthest corners of the galaxy. He found it extremely surprising to see her. "Tali? What brings you to Freedom's Progress?"

"I think a better question is how are you still alive . . . and with Cerberus." She had taken a step back, still cautious if this was all a trick. She was familiar with practically all things mechanical and technical, and she wouldn't put it past a demented group like Cerberus to have created some sort of clone or other of the greatest human warrior she'd ever known. Shepherd merely smiled at her before responding. "Cerberus put me back together. In return, I'm checking out the disappearance of human colonies."

"Don't trust him, Tali." The quarian Tali had just called Prazza, interrupted. She turned back towards him, her momentary distrust of the commander instantly vanished when he questioned her decision-making. "Commander Shepherd was the one who gave me the data on the geth in the Armstrong Nebula. I have every reason to believe him."

Tali turned back to her old friend. He had not considered the possibility that she would command a unit. Then again, her father was the leader of the Admiralty Board of the quarian Migrant Fleet. Leadership probably came naturally to her. "I'd like to help you, but we are looking for someone here on your colony. Another quarian named Veetor."

"Do quarians normally find there way to human colonies?" Jacob asked, honestly unaware of their culture.

"Veetor was on his Pilgrimage. He felt secure helping more secluded locations where there are fewer people around. The point is that he's still here, and we need to find him."

"Do you think he's the one that activated the mechs?" Samus was next to inquire Tali.

"Unfortunately. He is a bit unstable as well, and he suffered some damage to his suit. We believe that the subsequent infection has made him even more so."

"If he was here when the abductions happened, we'll need to talk to him." Miranda deduced. Tali was not yet ready to seal any deals. "Shepherd, I would appreciate your help, but if you are with Cerberus, I have to know now whether or not you're going to prevent us from taking him back to the flotilla."

"You know I'm not going to stop you. What could Cerberus have done to make you think that?"

"An attack on our fleet and the deaths of our people." Prazza interrupted again. Tali nodded in confirmation.

"That's not exactly what happened." Miranda felt the need to defend her boss again showing her fierce loyalty to him. Samus rolled her eyes. "With the way the Illusive Man run things, I wouldn't be surprised if it's _exactly _what happened."

Miranda gave her a cold stare, but Samus' armor must have reflected it because she couldn't have cared less. Shepherd quickly cooled the situation before it got out of hand. "The sooner we help you, the sooner we can find out what happened. What's your plan, Tali?"

Tali sort of shrugged. "He was last seen at the cargo docks. We aren't as well-equipped to deal with all the mechs. If you can head out first and draw their attention, we'll sneak around and try to get to him."

"And have us do all the dirty work? Typical quarian plan." Miranda rolled her eyes as she heard it. Prazza only became more angry. "Your friend's companions are only giving me more reason to not trust him. Why do you insist on having us do so?"

Tali grunted in annoyance. "Because I trust the commander more than I trust you."

That shut him up. Though Shepherd couldn't see past his suit's visor, he could tell he was furious by her remark. He turned to face Tali once more before preparing to head out. "We'll do it. Keep in radio contact should anything come up."

"On it, Shepherd." Tali took that moment to talk to her troops in private as the humans left.

Samus took the point this time while Shepherd took a step back to guard the rear. The fire team was no more than a hundred yards away from Tali before they heard her over their comms. "Watch out, Shepherd. I'm detecting a number of assault drones heading your way."

Almost as if on cue, a number of drones flew overhead and began to set themselves up along the tops of several buildings and structures. They began to bare their weapons on them, but the four humans were able to find cover before they opened fire. Shepherd replied back in mild sarcasm. "Thanks for the heads up, Tali."

Samus took a quick glance over her cover to check the drones' positions. They immediately opened fire on her. Her reflexes allowed her to drop back down before taking any damage to her armor.

"Enjoying the view?" Miranda asked, not even attempting to mask her taunt. Samus just ignored her to speak to Shepherd. "Three of them are standard assault drones, while two are of the rocket variant. If you can draw their fire for just a couple seconds, I can get behind them before they can react."

Shepherd nodded. "Shields won't last long with the rocket drones. I'd estimate about five seconds before we drop back down."

"That's all I'll need." Without another word, Samus' armor morphed into a perfect sphere about a meter in diameter. Shepherd was stunned, but remembered the plan they'd made. He signaled for his companions to open fire one the drones. They held their own for a couple seconds, but soon found their shields weaning and dropped back down. They had downed one assault drone and heavily damaged one of the rocket drones. After waiting for approximately a minute, they heard the sound of Samus' wave beam and all the drones being destroyed. Shepherd heard over his comm, "All clear."

Shepherd was the first to get back up. Unlike his companions, he was able to retain his composure when he found himself staring at Samus as she approached them from atop the buildings. Jacob was quicker to the punch in asking her, "How the hell did you do that?"

Samus dropped to their level and continued taking the point along the given path. "Came with the suit. Of course, it takes years of practice to perfect it."

Shepherd found himself smiling as the rest of them got back into formation. He couldn't help himself even as a small chuckle exited his lips. The others noticed, but felt no need to acknowledge it. They proceeded to follow Samus' lead. They soon reached a large door sectioning off their area when they could hear Tali over their comms again. "Shepherd! Prazza and his men have moved ahead. I told them to stop, but they wouldn't listen. They still don't trust you to give us Veetor when you're done."

"Of course," Miranda declared, almost rolling her eyes. "And we didn't even make a move against them. Just like the flottila incident."

"I'm really starting to dislike you, Miranda." Samus stated.

"Really? I started the moment the Illusive Man told me to make room for you onboard _my _station."

"Is this really the time for that?" Jacob was getting tired of the two women bickering.

"What's worse," the quarian continued. "A pair of YMIR mechs are guarding the security unit that Veetor is in. They still refused to listen to me."

Shepherd spoke back to Tali. "Tali, we have a sealed door in front of us. If you can open it, we'll try to help them while there's still time."

"All right, Shepherd. Give me one moment."

Shepherd turned back to his allies. "Get ready for a breach maneuver. Miranda and Jacob, take each side of the door. I'll be behind this barricade. Samus, can you detect the YMIR mechs past the door?"

"No. Their heat signatures are much milder than ours. However, I'm detecting the quarians. They're pretty far to the left of the door in guarded positions firing towards the right."

"Good to know. I want you to do what you did last time and try to get around them for another flank."

"On it."

They all got into their positions and waited for Tali. Just as she'd promised, the door slid open for them. Shepherd could visually see one of the YMIRs pounding at the quarians who were taking cover inside a residential unit. He zoomed in with his newly equipped sniper rifle and fired a round into its head.

His helmet's heads-up-display indicated that its shields were now gone and the armor was beginning to chip away. Both Jacob and Miranda began firing away with their own weapons to help bring the beast of a machine down. The mech began to turn its attention towards its newer, more aggressive opponents. By then, however, one of the quarians had launched a missile directly into it. The blast knocked the droid to the ground. It tried to set itself back up, but the constant fire made quick work of it. The explosion was pretty well controlled.

Just as Shepherd was about to have his team move forward, a missile soared straight into the quarians cover. He could see them all fall over, and hoped they weren't dead. Within moments, the second YMIR mech made its appearance from the far side of the cargo bay, originally unseen behind a different residential unit. With the quarians down, it turned to face Shepherd. A constant barrage of fire forced him and the others to keep their heads down.

"Where the hell is that stupid bitch!" Miranda shouted over the fire, obviously referring to Samus. Almost as if on cue, a large explosion was heard coming from the YMIR. Jacob stood up to look, but quickly dropped back down when he noticed the obscene amount of shrapnel flying towards him. It was no exaggeration, as the mass that once composed of the YMIR was now nothing but scrap metal. When everything died down, they all got back up to see what caused it. To nobody's surprise, they saw Samus standing there staring at Miranda with the retort. "Look in the mirror."

Shepherd didn't bother to listen to the two argue. His concern was the quarians. He dashed up towards the building they were in to see if they were still alive. To his surprise, he saw Tali already there caring for them. "They'll be fine, I think. This is your chance to talk to Veetor. Please don't let what Prazza has done change your mind."

"You have my word, Tali." Shepherd said offering her a hand to stand. "I'm wouldn't go back on that."

She took his hand and helped herself up and headed towards a bag on the other side of the room. "I still need to help them. I have some medi-gel in my pack. You really should go."

Shepherd nodded and moved towards the security unit. Thankfully, the others were waiting for him and neither Miranda nor Samus were still arguing. When he arrived, he motioned them to open the door. What they found was not what they had expected.

Seated at a computer console was Veetor, talking to himself uncontrollably. "-Hidden, and no one can find me . . . not them . . . not anyone . . . can't afford to leave . . . must wait until it's safe . . . no, no, no! It will never be safe!"

Shepherd approached him slowly. "Veetor. It's okay, nobody's going to hurt you."

He didn't even hear him. The quarian was still sitting and staring and mumbling to himself. Samus made a suggestion. "Perhaps we could shut down the computer."

"That won't be necessary." Shepherd looked at his omni-tool and fiddled with it briefly. The multiple screens began to go static. It got Veetor's attention. He realized someone was behind him. When he turned, he was relieved to see humans. "They . . . they didn't take you? How is that possible?"

"Take us? We've only just arrived." Miranda was a bit puzzled. "You assumed we were one of the colonists?"

"So you . . . you didn't see. But I saw it. I saw everything!" He pointed back to the screens as he accessed a video log. It showed some horrendous alien creatures taking humans away. Their were also a number of weird insect-like creatures scurrying around as well. Jacob made the next observation. "This video footage is new. Perhaps we can recognize the species."

One of the monitors froze as it zoomed in on them. Miranda was the most surprised. "My! It looks like a Collector."

"Collectors? Don't they normally keep to themselves?" Samus asked in confusion.

"Normally, but they do come out of their holes for the occasional trade, normally in slaves." Jacob corrected.

"First came the swarms," Veetor explained. "They find you . . . freeze you . . . and then the Collectors come and take you away. I analyzed them the best I could. The data is here on this omni-tool."

He offered it up to Shepherd, who took it without hesitation. "Thank you, Veetor. You have some friends outside who can take you back to the Migrant Fleet."

"You mean . . . Tali? She did come. It is safe then." He quickly ran out to find his comrades. Shepherd then turned to his companions. Miranda was displeased. "It would have been wiser to take him with us."

"For us, but not for him." Shepherd replied. "We'll do well enough with this information. Let's head back to gateway station. I'm sure the Illusive Man would be interested to hear about this."


	4. Chapter 3: Friendly Faces

Chapter 3: Friendly Faces

Once again, the chamber emitting the display of the Illusive Man had not changed. There he sat, smoking another cigarette (or was it the same one?) in that chair casually looking over Shepherd before finally responding. "Shepherd, I'm glad you took the time to go to Freedom's Progress. The information we found on the quarian's omni-tool has proven quite useful."

"Yeah, well it helps to have friends that can trust you." Shepherd did not attempt to hide the condescension in his remark. "I'd think it might turn your business around."

"Diplomacy is good when it works, but too much time talking can lead to inaction, something we can't afford especially now with the stakes so high." The Illusive Man paused a moment as he took another smoke. "Let's move on to the subject at hand. The information you obtained confirmed that the Collectors are behind these abductions."

"Confirmed? So you knew all along?" The soldier did not like being toyed with.

"I had my suspicions, but we needed proof."

"Okay, so now we know the Collectors are abducting our colonies. How does that involve the Reapers?"

"If you're still hesitant on this, then I see no point in trying to convince you of it. Regardless of who is controlling the Collectors, they are _still_ abducting our colonies, and it's something we can't ignore."

For once, Shepherd was a bit unsure of himself. If the Illusive Man couldn't prove the Reapers were involved, should he continue to help him? Entire human colonies were missing, and the council continued to ignore them. Helping humans . . . no . . . helping the galaxy was always a priority for him. He felt ashamed that he had forgotten that for a moment. "Okay, I'll help you. How do we get the Collectors?"

The Illusive Man grinned smugly, now having Shepherd under his hat. "The Collectors hail from beyond the Omega 4 Relay. If that doesn't ring a bell, it's a relay that no vessel has ever returned from save for their own."

"Any ideas why?"

"Nothing concrete. For the time being, my experts will continue to work on finding a way past the relay. As for you, you'll need a new team. I have constructed a list of scientists, mercenaries and specialists who would be useful for you mission. I'll be sending you their dossiers for you to look over."

"Thanks, but I prefer my old team."

"Your _old team_ was disbanded when you were killed. Since then, they have either dropped under the radar, or are engaged with other affairs."

"I just met up with Tali. Are you saying that was just a fluke?"

"Quite frankly, yes. Do not worry, these dossiers of people are not members of Cerberus, and if they give any respect to anyone, it will be to you, and not me."

Shepherd let out a sigh of contempt. "Very well. I suppose I'll have to take what I can get."

"Trust me, you'll be getting more than enough." Another smoke from his cigarette and he spoke again. "Two more things. You'll need a ship. I just ordered one that I think will suit you nicely and it should be docking with the station at this moment."

"And the last thing?"

"You'll need a pilot, and of this, I know you'll like him."

As if on cue, a familiar limping human entered the holoroom from behind. Seeing him again in one piece was a pleasant sight. "Hey, commander. It's just like old times."

"Now Shepherd," The Illusive Man said before fading away. "I leave you to your job. Make good use of your time and equipment."

With that, Shepherd was finally able to pat his old friend on the back. The limping man groaned. "Hey, watch it! I've still got brittle bones."

"Sorry, Joker. I just can't believe it's you."

They headed back out and towards the docking bay. "Look who's talking. I saw you get spaced. I don't see anyone else rising from _their_ graves."

"Got lucky. Cerberus patched me up." They took an elevator down to the docking bay. That's when Shepherd took the time to notice Joker's uniform. "So you joined up with Cerberus?"

"Hell yes, I did. After you died, theAlliancejust tried to shuffle us around and pretend nothing happened, as if they could hide the fact that you were dead. They even tried to ground me. I just didn't have any other options."

"I suppose I can't blame you," Shepherd nodded his head. Slowly and steadily, he was beginning to wonder if Cerberus was as bad as he had remembered, or if it was faulty regeneration. "But do you think you can trust them?"

Joker stifled a chuckle. "I don't trust _anyone_ who gets paid more than I do. But I gotta hand it to them; they saved your life, let me fly, and also, they got this . . ."

The elevator doors opened and they walked up to the window overlooking the docking bay. Through the window, Shepherd saw another familiar, yet, unique sight. TheNormandy, the ship that was destroyed, had been rebuilt. With Cerberus markings declaring it's allegiance, it almost looked as nice as the original, but Shepherd would leave his summation until after his inspection of it's insides. Still, it was a beautiful sight to behold.

As they were staring in admiration, Samus Aran approached them. "So this is your new ship?"

Shepherd turned to address her. "Yes . . . looks almost like the old one too."

"If it's all right, I'd like to have my ship moved into the hangar."

Now Joker was swayed to look at their new company. He began eyeing the armored figure closely, half in admiration and the other half in caution. It didn't stop the commander to consult his new pilot. "I don't know. Joker, could her ship fit in the hangar?"

"I'd need the dimensions."

Samus ran the numbers off for him. "Ten meters, by eight meters, by three meters."

Joker nodded towards Shepherd, who answered her question. "Sounds like it will. Once we've left the dock, we'll prepare for your arrival."

Samus thanked him before heading back towards her ship. Shepherd watched as she left. After watching her in combat, he felt good knowing that she had his back. Joker interrupted his train of thought. "Sure is beautiful, isn't she?"

"I wouldn't know. She's never taken the armor off."

"I was referring to the ship, commander." A sly grin streaking his face as he said so. Shepherd didn't even waver at the misunderstanding. He just started heading off towards their new ship. He couldn't wait to see what was inside.

* * *

><p>Commander Shepherd was surprised when he finally boarded his new ship. It's features were slick and new, while still holding onto that tinge of familiarity. The biggest surprises were his new quarters and the ships AI called EDI. His quarters were furnished like that of a luxury vessel, something that he never had the truly had before. It was new experience for him. As for the AI, as long as she was still restricted from controlling the ship, he'd be fine with her being around.<p>

While changing into more casual clothes, he looked over the dossiers that the Illusive Man had given him. He decided that their first stop would be Omega, the space station within the Sahrabarik system of the Omega Nebula. Several of the specialists were listed as being there, which would allow him to waste little time hiring people.

Once he had finished changing, he found himself wondering what to do next. He'd already spoken with Jacob and Miranda, whom had given their input on where to start. Miranda, being the highest ranking Cerberus officer, was made the XO of the ship, while Jacob chose a stance as the quartermaster. Both indicated they'd be busy for a while, and weren't free to speak to for long.

Among the other members of note were Yeoman Chambers, essentially a secretary and psych evaluator, Mess Sergeant Gardner, the ship's cook, Engineers Donelly and Daniels, constantly tweaking engine performance, and finally Doctor Chakwas, who was a former member of the original Normandy. Each made mild suggestions to help upgrade the performance of the ship (and its crew) in some minor way.

It seemed that all was well, and that he had some time to kill. Perhaps now he would have a chance to get some answers out their mysterious passenger. Samus Aran had her ship moved into the cargo hold, which is was the last time he'd seen her. He decided that now was as good a time as any.

With his mind made up, Shepherd entered the lift and headed down to the fourth deck. Once there, he navigated through the proper halls and passageways to reach the docked ship. The small yellow ship's lights were on, presumably because Samus was working inside. He pondered momentarily whether or not she'd notice him standing there, or if he should call her. Before having to decide, a lift lowered from her ship, revealing the armored figure. She slowly approached Shepherd, and sat on a couple of crates just a few feet away from him.

That's when she did the unexpected. For the first time since he'd met her, Samus took off her helmet. A long tail of golden blonde hair dropped from underneath. To his surprise, the warrior was not only strong and agile, but gorgeous as well. Perhaps he should not have been too surprised, since many women he's worked with were beautiful in their own right. Perhaps it was because of her fully armored exterior often indicated a more rigged look. This of course, was not the case. Needless to say, he was glad to see her loosening up.

"It's good to see what's behind the helmet for once." He commented. Then he added jokingly, "For a while I was wondering if you were even human underneath."

She replied with a small chuckle herself. "Sometimes I wonder that myself, as well."

Shepherd decided to take a seat on a couple of crates himself. Better to talk on the same level than to be above a person whom you are trying to get to open up. "Do you ever take the rest of your armor off?"

She nodded. "Back home, when things were calm, I'd almost never wear it. Still, during times of strife, I've felt really vulnerable without it."

"Are you?" Only a couple questions in, and he was already feeling for her. She attempted to defend herself at first, but quickly let her guard down. "Oh, no! At least, not completely. I'd suspect I'm stronger and faster than the average humanoid, but still . . . the universe is a dangerous place."

"Perhaps, but there's usually a place isolated from it all that you could escape to. Of course, if the Reapers are returning, I doubt any settlement's safe."

"That's one thing I believe coming from the Illusive Man."

"Did he do anything to you directly to make you think that way?" Despite his own experiences, he doubted they were anyway similar to hers.

"Mostly his operatives, though I doubt he wasn't involved as he claims. They wanted to examine my DNA more closely."

"Did it have to do with my revival?"

Samus nodded again. "It did. I don't like talking about it, but I've had some genetic tailoring to help me use this armor. It's why you don't see anyone else using anything like it."

"You mean it has certain biological features that make it work?"

"You're sharper than you look, commander." She replied, with a slight sass in her tone.

"Thanks," he replied, playing along. He also found himself subconsciously stroking his crew cut hair. "You don't have to call me that here."

"So what should I call you? Of all the people I know, you're the only one whom everyone calls by your last name. Why's that?"

"Military thing, I guess. If you prefer, you can call me John."

"All right, _John_." Samus took a deep breath before properly answering his previous question. "Anyway, the suit is capable of bonding with me. It makes it easier to access the numerous features in it."

"Interesting." Shepherd was deeply enthralled with this discovery. "But hold on. You mentioned earlier that you were infected by a parasite-like virus. Wouldn't that affect your suit?"

"For the one I was using, yes. Like I'd said, I eventually had to ditch it for this one. By that time, the parasite and the cell-based vaccine had run their course out." Samus placed a hand on her hip and tilted her head slightly. "You weren't here to ask about my armor, though, were you?"

"It was an interesting topic, but no, I wasn't." Shepherd leaned in to speak. "I'm more curious about whatever you did that brought me back and what affect it will have on me."

"If you're afraid of any drawbacks, don't be." She smiled slightly. It had been a long time since she'd felt so in charge when talking to a superior. "Though I doubt you'll be feeling any of these things, you might receive some enhanced reflexes. Possibly some added strength as well, but that really depends on you. The only thing I can guarantee is that your body will heal faster than ever before, and that you'll probably live another twenty to forty good years more than the average person."

"Good to know. But why did you do it?"

She froze, just as she had done before when the Illusive Man had asked her the same question. Though Shepherd didn't know, she still hadn't prepared herself to answer the question. Even if the summation was more than enough. "I- . . . I need you."

Shepherd's eyes widened in surprise. Samus tried to correct herself. "I mean-! Ugh! What I meant was that . . . _we_ need you."

Samus stood up, clasping her hand over her face in embarrassment. Then she dropped it as she fixed her mistake. "You're special, Shepherd. This threat of the Reapers is too large for any one single person, but there's an aura about you that compels people to follow your lead. No one else in the universe could lead theAllianceto defeat them."

Shepherd let a smile escape his lips. "I appreciate all the confidence you've put into me, but certainly I'm not so unique in the galaxy that no one else could try."

"Anyone could try, but they won't succeed. I have faith in your leadership and skill."

"I'm glad to know it. It's difficult to lead when your troops don't."

For a moment, it seemed as if they had nothing left to say. Then Samus piped up.

"A question, if I may, John?" He nodded. "Do you think any others from your old crew will join you if they know you're with Cerberus?"

"I'm not with Cerberus. We just have a mutual understanding. As for your question, I don't know. I would like to think they will, but it's different when the threat is not as visible as before."

"Well I hope they do. Considering what we _might_ be up against, we'll need every hand we can get."

Shepherd sighed while nodding his head. He had considered the possibility that a small team of specialists might not be enough. But the Citadel Council would never listen to him while he had any association with Cerberus. Slowly, he stood up and began to walk back to the bridge, muttering lowly under his breath, "I hope so too."


	5. Chapter 4: Rule of Omega

Chapter 4: Rule of Omega

If there was one word to describe Omega it was "vile". Although he had been anticipating his arrival on this station for the last couple of hours, nothing could quite prepare him for it. The place emitted a vile atmosphere that would attract only those whom detested people asking questions. Yet, that was one of the main reasons Commander Shepherd had to set foot on this god-forsaken station. He was appalled by the stench of narcotics that suddenly invaded his nostrils the moment he set foot inside the place. The only logical response he could think was to seal his helmet and filter them out.

Then he heard Jacob coughing several feet behind him. He had to cope without, something he probably should have thought about before leaving the ship. Miranda, whom had been to Omega before, appeared immune to the fumes, while Samus was obviously unaffected while still wearing the massive powersuit. Once Jacob had stopped coughing, Shepherd motioned for them to move along.

Before they even left the loading tunnel, they were approached by a salarian. One whom was too enthusiastic. "Hey there, travelers! First time to Omega? It can be a bit over-"

The small salarian was interrupted by a more massive batarian barging past him to meet up with Shepherd. He didn't even look past the little guy as he spoke directly to the commander. "Well, _Commander Shepherd._ So you've come here to Omega?"

"You know me?" Shepherd inquired slightly annoyed that his return wasn't as secret as he'd hoped.

"Of course I know _you_, human. We've had your ship tagged the moment it entered the sector." The batarian explained, slightly annoyed that Shepherd had returned to life. "That doesn't matter. You need to see Aria in Afterlife before you do anything here."

"Before we do anything? Is she expecting us to cause some trouble?"

"Do you need me to answer that question?" The batarian waited for a response, but Shepherd only shook his head. "Like I said. Afterlife. Now."

The batarian walked away grabbing the salarian as he left who protested all the way. Shepherd looked towards his team. "Sound like a trap to you?"

"Aria is not one to kill on a whim," Miranda explained. "If anything, she'll just want to make sure we don't make any problems for her."

"She owns the place?" Shepherd asked further. Miranda shook her head. "But she might as well."

"Then I suppose we shouldn't keep her waiting." With that, he continued down the pathway towards the rest of the station. Almost instantly after exiting the docking bay, the night club known as Afterlife could be seen ahead no more than a hundred yards away. Shepherd wasted no time trekking up the steps past the usual line of patrons being held back by an elcor bouncer. Shepherd could hear a human argue with the bouncer, not a good idea.

As they passed through the large doors, they found themselves in another passage way just outside of the main club area. A few patrons were seated drinking, mostly batarians. Shepherd had a natural distaste for batarians, but did his best to avoid confrontation with them regardless. Still, his efforts remained fruitless as a small group of batarians rose from their table and approached them. One wearing blue spoke for the group. "And what are a group of _humans_ doing here? We don't like your kind, so I suggest you leave before things get ugly."

Shepherd played it cool despite the obvious trigger-happy attitude of his adversaries. "If things do get ugly, it's not me that's going to regret it. Certainly you can tell we're not your average human rabble."

He gave the pistol at his side a rub with his index finger, just for good measure. The batarian took a look, and realized that he and his compadres were outmatched. Without even a proper retort, they headed back to their seats. Shepherd took his cue to hurry in before they changed their mind. Behind him, he could hear Samus complimenting him. "I'm impressed, Shepherd. That was really nice of you to let them live."

Shepherd grinned slightly. "I'm just not in the mood right now for trouble. If possible, I'd just like to hire these specialists and get out with no conflicts whatsoever."

"If only things _were_ that easy." Jacob remarked.

The next door led into the main club. Asari dancers could be seen above the bar moving to the pulsing rhythm of the music throbbing through the ears of everyone who was in Afterlife. The place was full of life as people were laughing, dancing, and shouting all over the place. Shepherd noticed the elevated platform on the other side of the bar and proceeded to head over their, assuming that it was where their mysterious host.

The four humans approached the platform and the figure could more easily be seen. It was an asari, as expected, whom although was not facing them gave off an aura of an executive business woman. Just before he reached her, they were halted by her security chief, another batarian. He also heard the asari speak firmly against him coming closer. "Stay where you are, Shepherd, and I'll decide whether or not you're allowed on my station."

The batarian began to scan the commander and his companions. The others were told to stay further away while negotiations would be made with Shepherd. Shortly, the batarian finished his scans. "It's him, alright."

That's when the asari turned to face the commander. She had a couple of facial tattoos that supported her determined, business-only appearance, and reminded Shepherd to at least be polite enough not to piss her off. "I was told you wanted to see me."

The asari sat down on the luxurious couch at the edge of the platform, facing the commander. She motioned for him to sit as well which he did so, but at a relative distance. Then she finally spoke up. "Let's just say that when word is passed that the Hero of the Citadel might be alive, and just so happens to show at my station, I get curious. You're not here to just relax and 'shoot the breeze' like the others. You're here looking for something. I believe the best way to ensure you don't go asking around the wrong people and causing messes is to talk directly to me."

"So you _do_ own Omega."

She chuckled at the thought before standing up and turning back to the station beyond the platform, with the dramatic rise of her hands, she stated. "I _am_ Omega."

Aria turned back Shepherd and step towards him, she placed one of her high-heel booted feet uncomfortably close to him. "And I like to keep it that way. I just want to make sure that you know the rule around here before you go blasting your way around."

"And that rule is?" Shepherd asked, not intimidated by her proximity. Aria sat back down in a relaxed pose and raised a single finger. "Don't fuck with Aria."

Shepherd held back a chuckle himself, but nodded his head in acknowledgement. "All right, Aria. I'll keep my distance, but I expect the same from your goons."

"Then we are in agreement." She smiled smugly as she took a sip from a drink she had next to her. "So what exactly _are_ you looking for?"

"Specialists. I'm recruiting for a hazard op and I need some elite personnel. _Non-military_ personnel."

"I'm sure you can find plenty of scum willing enough to sign up for your suicide run if you raise the price enough."

"Not what I'm looking for. I already have dossiers on the two I'm looking for. I need Dr. Mordin Solus and the mercenaryArchangel."

"Those two? Well I might be able to help you with Dr. Solus, butArchangelis being a bit elusive at the moment."

"And why is that?" Shepherd pondered aloud. Aria couldn't help but let her smile widen as she explained. "Because he's pissed off every major mercenary group here. I expect he'll be laying low for a while. Perhaps if I catch wind of him, I'll let you know."

"That'd be appreciated. What about the doctor?"

"He's got a clinic in the Gozu District. Of course, those slums have been quarantined since the plague began."

"There's a plague in the slums? Is Mordin trying to suppress it?"

"From what I've gathered, he's close to making a cure. If you wait a while, you might be able to see him."

"We can't afford the wait. If my team got in hazard suits, would allows us to go in? We'd be quick to assist him in finishing the cure."

"And I suppose you have medical staff suited to do so?" Aria sarcastically asked. She shook her head briefly. "Whatever, humans are immune to the virus. I'll let go if you must, but you won't come back in until that plague is gone. Are you in that much of a hurry?"

Shepherd nodded solemnly. The asari sighed in response. "Very well. Tell the guard at the slums entrance that I've given you permission."

Shepherd stood up, and with a mild bow of respect, thanked her for her assistance. He then returned to his crew. They walked briskly out of the club while Shepherd explained their destination. The others agreed to his plan of action, and were quick to follow. Still, the situation in the slums was curious. It was left for Jacob to pop the question in everyone's mind. "Why do you suppose the virus doesn't affect humans?"

"Humans do have a varied immune system," Samus conjectured. "Some things that effect other species greatly don't effect us at all, as the reverse is often true. It's also possible that a human designed it."

"And release it in the Gozu District?" Miranda queried. "What would they gain by doing that? It makes little sense for a sophisticated human scientist to release a plague there."

"Unless he or she were to test the effects of it." Samus countered. It detracted Miranda slightly to hear the armored figure still attempt to disprove all of her hypotheses, but Samus didn't seem to be too interested this time. Miranda considered to continue to defend herself, but eventually decided against it. Within several minutes, the squad reached the door to the Gozu District. A turian guard was holding off a human woman from entering. They were arguing back and forth for awhile by the looks of it.

"Sure," the guard spat. "Of _course_ you just want to get your stuff, and probably the stuff of a dozen other dead citizens. Probably caused it too, didn't you?"

"Asshole!" The woman rebuked. "Why the hell would _I_ do something as stupid as this? I've got friends who _aren't_ human, you know. Besides, the vorcha are immune too. Why don't you talk to _them_ about the virus?"

"Because they're on the inside, and I'm staying on the outside."

Shepherd politely stepped between the two. "I understand that the situation is pretty dire, but Aria just told me that my team can go through."

"You spoke to Aria?" The guard was rather impressed, but not quite convinced. "And what did she expect you to do?"

"Nothing, really. What we _plan_ to do is another. We're here for Mordin Solus. As soon as he creates a cure, we'll be on our way out with him."

"That crazy doctor? Hell, I'd be glad to see him go. But if you go in there, I'm not letting you back in until I'm told to open the place up."

"That's fine with us." The guard stepped aside for Shepherd and his team. The woman tried to go in with them, but the guard stopped her again. "Oh, so _they_ can go in but I can't. Oh! I forgot to tell you that Aria said _I_ could go back in too!"

"Yeah, right. Whatever."

* * *

><p>And Samus thought that the <em>main<em> part of Omega looked and smelled awful. The slums were another story entirely. Miranda was able to sum it all up in a single word: pisshole. She couldn't help but agree with her. There was _nothing_ appealing about this place. How a salarian doctor could set up a clinic here was . . . well it made perfect sense, but how someone was capable of pulling it off was different. Samus couldn't help but admire the amount of dedication it must have taken for Dr. Solus to take on such a task.

Immediately after being allowed past the border guards, there were signs of riots. Trails of blood, dead bodies and burned out electronic panels to people's homes. the place really had gone to hell since the plague had began. Shepherd still took the precaution of wearing his helmet, as did the Cerberus agents, just in case an alteration to the disease had been made to affect humans.

After turning down a hallway, they spotted several Blue Sun mercenaries coming out of an apartment unit with their new trove of stolen goods. One of them, a batarian, noticed the newcomers and instantly began to pull his pistol. Samus halted him in his tracks with a cold blast from her ice beam. The others, now alert to the intruders, dove for cover and began to fire back. Commander Shepherd and Miranda ducked around some nearby crates while Jacob hit the dirt in a prone position. Samus took the opportunity to finish the frozen thug with a missile before finding a pillar to hide behind.

The firefight didn't last too long, as the other batarians of the Blue Suns were sick, and not fully competent, while the humans were simply _in_competent. A few barrages of fire from Shepherd's assault rifle and Miranda's submachine gun kept there heads down while Jacob and Samus got close enough to finish them off quickly.

As they reformed, Samus noticed a bystander. A sickly batarian whom was probably the victim to the Blue Suns robbery. She pointed him out to Shepherd, who decided to approach him. The batarian didn't seem to have any trust in human kindness. It raised a pistol with weakened fingers at them. "Keep away, humans! I know . . *_cough_* . . what counts as 'hospitality' amongst your kind."

Shepherd wasn't afraid of him firing, but he didn't want to alarm him when it wasn't necessary, so he holstered his weapon as he spoke. "You look injured. Do you need any assistance?"

"No . . *_cough_* . . no injury. Just this damn plague. Why should you care? You're kind . . *_cough_* . . caused it."

"I'm not a resident here. I'm looking for Mordin Sol-"

"I said keep away from me! Don't think that I . . *_cough_* . . that I . . *_cough_* . ." The batarian lowered his arm as it fought the disease that was slowly killing him. Shepherd made no hesitation as he kneeled down and applied a medi-gel for him. "Hey! Stay with me!"

As the medi-gel kicked in, the batarian found himself strong enough to stand. "You . . . saved me?"

"I'm not here to kill. I'm here to help. That medi-gel won't cure you but it should relieve some of the symptoms for now. I need to find Dr. Mordin Solus' clinic. Do you know where it is?"

"Yes. It's farther down this hallway and across theAzuBridge. But I wouldn't trust that doctor if I were you."

"And why is that?"

"Because he's ruthless." The batarian sounded slightly scared at the mention. "I saw a group of Blue Sun mercs try to shake him down for protection. He had them all shot."

"Even still, he's developing a cure. If I get there, I'll have someone come and get you." Shepherd turned and began to leave, but was halted shortly after. "Wait, human. I . . . I should thank you."

"It's okay." Shepherd told him and he carried on his way.

Seeing Shepherd continue to diffuse sticky situations with mere words amazed Samus. As good as she was at analyzing people and cultures, she still couldn't get a bead on how he was able to do it. Was it the military training, his spacer upbringing, or did it just come naturally to him? Despite her seeming ineptitude, she was glad that she had picked the right man to follow. She had not had a commander of such high caliber since Adam Malkovich.

But Shepherd was different. Whereas Malkovich was more of a father figure, Shepherd was more of a . . . what? Brother? Friend? No they didn't fit either descriptor. Of course, that left one particular possibility, but she shuddered to think of it. There was no way that it could possibly be that. She quickly brushed such thoughts away, knowing that they were just childish.

Samus took the point as they passed theAzuBridge, hoping to detect some new targets to give her a new focus. This was to no affect. After turning around another corridor of halls, the team discovered a pair of YMIR mechs guarding a door with a man behind a shatter-proof window monitoring them. Shepherd approached them calmly, noting the sign above indicating that it was the clinic.

The man eyed them wearily, but seeing that they weren't wearing any mercenary insignias, he waved them through with a warning. "Keep your weapons holstered and cause no problems, or else we'll _have_ a problem."

Shepherd nodded politely as he entered then now opened doors. Knowing that she couldn't 'holster' her cannon, Samus just kept her arm at her side as she sauntered in behind him.

The clinic was full of patients. A number of nurses tried to help those who were ailing the most, while the others waited by. Coughing was the most common sound to be heard. Samus couldn't help but stare at the copious amounts of people, feeling pity for those who've had to go through what she could only imagine was a painful experience.

Shepherd, however, was a little more preoccupied looking for Mordin Solus. He followed a few passageways until he thought he could here the sound of the salarian giving out a prescription. As he turned the last corner and entered the closest room, he saw him.

The description in the codex Samus had was to generous, showing off his picture from a time when he must have been a younger, keener medical officer. The salarian bent over a mix of chemicals was far older. The wrinkles of time shown on his face quite clearly, even from the eschewed perspective. Yet, despite the age, the hands of the doctor were fast and unwavering, moving as if by instinct rather than thought.

"Professor Mordin Solus?" Shepherd asked respectively. The doctor turned from its work hearing the unfamiliar voice calling his name. He took a second to study the man asking him before beginning a nonstop barrage of questions which he'd answer himself. "Armed soldiers. Quarantine still in effect, yet not wearing mercenary uniform, yet clearly outsiders . . ."

With this rant, Samus was able to realize that he most certainly was a creature of thought and not instinct. He simply thought faster than the average human. Not to mention out loud as well. As interesting as this was, she felt a need to put a stop to it. "Professor, you can calm down. We're here to ask for your help . . . outside of the current viral outbreak."

"Oh?" The professor eyed them again. "Freelance soldiers working for large corporation?"

"Ever heard of a group called Cerberus?" Samus spoke before Shepherd or Miranda could say anything, ensuring that he knew who exactly they worked for. Mordin was well informed. "Quite. Heard they only worked with humans. Branching out, it seems? Must be something important if so."

"It is." Shepherd finally got a word in, eyeing Samus and letting her know that he would take it from there. "The Collectors have been abducting entire human colonies, using technology and bioweapons that we've never seen before. You were at the top of the list of specialists who would be more than qualified to assist."

"Hmm . . . Collectors. Our goals may be similar. Virus created by an unknown assailant. Collectors perhaps the only race with technology to develop it." He put a three digit hand to his chin as he pondered the thought, but he quickly stopped as he remembered his current objective. "Discussion will have to wait. Have cure to virus now. Need to get it to the ventilation systems blocked by vorcha."

He turned his head to the Commander before finally saying, "Need to kill them."

Shepherd took a step forward, ready to speak again, but then a noticeable fluxuation in the room's lights halted him. The air also became slightly more stale, something he never thought he would have been able to pick up before. Mordin consulted his omni-tool before recognizing the problem. "Ventilation has shut down. Vorcha trying to prevent cure. Need to stop them now."

Mordin started moving hectically around his office, gathering supplies and the like. Shepherd took this as an opportunity to stand in his way, getting his full attention. "Give me the cure. My team and I will go ahead and take care of the vorcha. Your job is here with your patients."

Mordin nodded, adhering to his advice. "Very well. I'll stay back with them."

"Good." Shepherd started out before he remembered something. "Oh, I also met a batarian near the entrance of the district. He's too sick to make it here on his own."

"I'll have a mech sent to escort him. Similar note, my assistant, Daniel, went into vorcha territory looking for batarians. Hasn't come back in some time. If possible, keep an eye out on him."

"Will do." Shepherd finally, made his way out of the office with his team. "Let's go, team."


	6. Update

**UPDATE**

I deeply apologize that I have to make this announcement (it's going to sound like a dirty Dear John letter), but it seems that I must. This story-Mass Effect 2: Factor X-is essentially dead. I know that many of you have shared your enjoyment that you've had with the story, but I'm afraid that I can't keep working on it, and there are two reasons why.

First: My schedule is no longer as free as I'd like it to work on three different stories at once. Heck, just working on 'Sorrow of Silidan' is enough to keep me swamped. Therefore, I had to stop work on at least one.

Second: This story is actually...well...ordinary. By that I mean, yes, it's a fun, adventurous crossover, but not much else. I like to at least make my work more significant. Think the difference between 'Seven Samurai' and 'The Magnificent Seven.' They're both great movies, but 'Seven Samurai' is more than just that. I am being rather presumptuous to compare my works to 'Seven Samurai' (I KNOW it's never going to be that good), but I find it important for you, the reader, to understand what I feel.

I started this project simply because I had an idea in my head, and decided to write it down. Unfortunately, that idea could not develop into something more intriguing than "Samus Aran is in Mass Effect 2." Quite frankly, ANYONE can write that story. While my style may be more interesting (I only assume because of all the 'favorites' and reviews), it's really a simple plot, and the story is already known to most fans.

I feel really bad that this project must be placed on an indefinite (and most likely never-ending) hold, and almost wish that I'd never started it in the first place, but it's here, and the effect has already spread. If this really saddens you, I am incredibly sorry, but this must be.


End file.
